package org.cbioportal.legacy.web;

import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.Parameter;
import io.swagger.v3.oas.annotations.media.ArraySchema;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
import io.swagger.v3.oas.annotations.responses.ApiResponse;
import io.swagger.v3.oas.annotations.tags.Tag;
import jakarta.validation.constraints.Max;
import jakarta.validation.constraints.Min;
import jakarta.validation.constraints.Size;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.cbioportal.legacy.model.CopyNumberSeg;
import org.cbioportal.legacy.service.CopyNumberSegmentService;
import org.cbioportal.legacy.service.exception.SampleNotFoundException;
import org.cbioportal.legacy.service.exception.StudyNotFoundException;
import org.cbioportal.legacy.web.config.PublicApiTags;
import org.cbioportal.legacy.web.config.annotation.PublicApi;
import org.cbioportal.legacy.web.parameter.Direction;
import org.cbioportal.legacy.web.parameter.HeaderKeyConstants;
import org.cbioportal.legacy.web.parameter.PagingConstants;
import org.cbioportal.legacy.web.parameter.Projection;
import org.cbioportal.legacy.web.parameter.SampleIdentifier;
import org.cbioportal.legacy.web.parameter.sort.CopyNumberSegmentSortBy;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.validation.annotation.Validated;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestAttribute;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;

@PublicApi
@RestController()
@RequestMapping("/api")
@Validated
@Tag(name = PublicApiTags.COPY_NUMBER_SEGMENTS, description = " ")
public class CopyNumberSegmentController {

  private static final int COPY_NUMBER_SEGMENT_MAX_PAGE_SIZE = 20000;
  private static final String COPY_NUMBER_SEGMENT_DEFAULT_PAGE_SIZE = "20000";

  @Autowired private CopyNumberSegmentService copyNumberSegmentService;

  @PreAuthorize(
      "hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/studies/{studyId}/samples/{sampleId}/copy-number-segments",
      method = RequestMethod.GET,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(description = "Get copy number segments in a sample in a study")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content =
          @Content(array = @ArraySchema(schema = @Schema(implementation = CopyNumberSeg.class))))
  public ResponseEntity<List<CopyNumberSeg>> getCopyNumberSegmentsInSampleInStudy(
      @Parameter(required = true, description = "Study ID e.g. acc_tcga") @PathVariable
          String studyId,
      @Parameter(required = true, description = "Sample ID e.g. TCGA-OR-A5J2-01") @PathVariable
          String sampleId,
      @Parameter(description = "Chromosome") @RequestParam(required = false) String chromosome,
      @Parameter(description = "Level of detail of the response")
          @RequestParam(defaultValue = "SUMMARY")
          Projection projection,
      @Parameter(description = "Page size of the result list")
          @Max(COPY_NUMBER_SEGMENT_MAX_PAGE_SIZE)
          @Min(PagingConstants.MIN_PAGE_SIZE)
          @RequestParam(defaultValue = COPY_NUMBER_SEGMENT_DEFAULT_PAGE_SIZE)
          Integer pageSize,
      @Parameter(description = "Page number of the result list")
          @Min(PagingConstants.MIN_PAGE_NUMBER)
          @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_NUMBER)
          Integer pageNumber,
      @Parameter(description = "Name of the property that the result list is sorted by")
          @RequestParam(required = false)
          CopyNumberSegmentSortBy sortBy,
      @Parameter(description = "Direction of the sort") @RequestParam(defaultValue = "ASC")
          Direction direction)
      throws SampleNotFoundException, StudyNotFoundException {

    if (projection == Projection.META) {
      HttpHeaders responseHeaders = new HttpHeaders();
      responseHeaders.add(
          HeaderKeyConstants.TOTAL_COUNT,
          copyNumberSegmentService
              .getMetaCopyNumberSegmentsInSampleInStudy(studyId, sampleId, chromosome)
              .getTotalCount()
              .toString());
      return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
    } else {
      return new ResponseEntity<>(
          copyNumberSegmentService.getCopyNumberSegmentsInSampleInStudy(
              studyId,
              sampleId,
              chromosome,
              projection.name(),
              pageSize,
              pageNumber,
              sortBy == null ? null : sortBy.getOriginalValue(),
              direction.name()),
          HttpStatus.OK);
    }
  }

  @PreAuthorize(
      "hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/copy-number-segments/fetch",
      method = RequestMethod.POST,
      consumes = MediaType.APPLICATION_JSON_VALUE,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(description = "Fetch copy number segments by sample ID")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content =
          @Content(array = @ArraySchema(schema = @Schema(implementation = CopyNumberSeg.class))))
  public ResponseEntity<List<CopyNumberSeg>> fetchCopyNumberSegments(
      @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface
          @RequestAttribute(required = false, value = "involvedCancerStudies")
          Collection<String> involvedCancerStudies,
      @Parameter(
              hidden =
                  true) // prevent reference to this attribute in the swagger-ui interface. this
          // attribute is needed for the @PreAuthorize tag above.
          @RequestAttribute(required = false, value = "interceptedSampleIdentifiers")
          List<SampleIdentifier> interceptedSampleIdentifiers,
      @Parameter(required = true, description = "List of sample identifiers")
          @Size(min = 1, max = PagingConstants.MAX_PAGE_SIZE)
          @RequestBody(required = false)
          List<SampleIdentifier> sampleIdentifiers,
      @Parameter(description = "Chromosome") @RequestParam(required = false) String chromosome,
      @Parameter(description = "Level of detail of the response")
          @RequestParam(defaultValue = "SUMMARY")
          Projection projection) {

    List<String> studyIds = new ArrayList<>();
    List<String> sampleIds = new ArrayList<>();

    for (SampleIdentifier sampleIdentifier : interceptedSampleIdentifiers) {
      studyIds.add(sampleIdentifier.getStudyId());
      sampleIds.add(sampleIdentifier.getSampleId());
    }

    if (projection == Projection.META) {
      HttpHeaders responseHeaders = new HttpHeaders();
      responseHeaders.add(
          HeaderKeyConstants.TOTAL_COUNT,
          copyNumberSegmentService
              .fetchMetaCopyNumberSegments(studyIds, sampleIds, chromosome)
              .getTotalCount()
              .toString());
      return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
    } else {
      return new ResponseEntity<>(
          copyNumberSegmentService.fetchCopyNumberSegments(
              studyIds, sampleIds, chromosome, projection.name()),
          HttpStatus.OK);
    }
  }
}
